The Query screen is the first of four screens in the BLAST Search wizard. The Query screen is where you add the query sequence, i.e., the sequence for which you wish to locate matches in the NCBI BLAST database.

At the top of the screen, next to “Search with,” select the Nucleotides or Proteins button.

To add one or more query sequence files or a folder of sequences:

Press the Add or Add Folder buttons. In the file explorer, navigate to and select the desired file(s)/folder(s), and then click Open. If you add a multi-file sequence or multiple sequences, each sequence will appear on a separate row in the table.

To paste or type in the query sequence:

Press Enter.

In the Enter dialog:

  1. Type or paste in the desired sequence following the “dimmed” example in the dialog. A header line is optional.

  2. (optional) If you wish to use only a range of this sequence, specify the Start and End positions.

  3. (optional) If you want to add another query sequence after this one, check the Add another box. After clicking OK to the first sequence, a new Enter dialog will open to add the next query. Otherwise, leave this box unchecked.

  4. Press OK. If you add additional sequences, each sequence will appear on a separate row in the table.

To remove a file that has already been added:

Select the unwanted file from the list and click Remove.

To learn about the optional tools in the bottom left corner of the screen, see the bottom of this topic.

Once you have set up the query sequence(s) as desired, do either of the following:

  • To choose the BLAST program to use and database to search, press Next to continue to the Search screen.
  • To run the search directly, press Run.
  • To close the Search wizard without starting a search, press Cancel.

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